A high-quality, chromosome-scale genome assembly of the shade-tolerant wild rice, Oryza granulata

Abstract

Oryza granulata Nees et Arn. ex Watt, a diploid wild rice (GG genome), possesses exceptional shade tolerance and is a key genetic resource for rice improvement. However, previous genome assemblies lacked continuity and completeness. Here we present a chromosome-scale reference genome of O. granulata using PacBio SMRT (113x), Hi-C (95x), and Illumina sequencing. The final assembly is [~]764.24 Mb, with a scaffold N50 of [~]59.32 Mb, and [~]96.47% of the sequence anchored to 12 chromosomes. BUSCO completeness is [~]98.6%. We annotated [~]42,064 protein-coding genes, of which [~]95.39% were functionally annotated, along with [~]73.46% repetitive elements. The genome assembly and raw sequencing data are available at NGDC (PRJCA061980), NGDC GSA (CRA041662), and NGDC GWH (GWHISVE00000000.1). This high-quality genome will serve as a fundamental resource for evolutionary genomics, conservation biology, and breeding of shade-tolerant rice cultivars.